cran: MCL | Projects | Ecosyste.ms: Papers

10.1093/molbev/msx090

Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins
Cited by: 12
Author(s): Raquel Dias, Austin R. Manny, Oralia Kolaczkowski, Bryan Kolaczkowski
Software Mentions: 1
Published: over 7 years ago

10.1093/molbev/msv081

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing
Cited by: 183
Author(s): Ya Yang, Michael J. Moore, Samuel F. Brockington, Douglas E. Soltis, Gane Ka‐Shu Wong, Eric J. Carpenter, Yong Zhang, Li Chen, Zhixiang Yan, Yinlong Xie, Rowan F. Sage, Sarah Covshoff, Julian M. Hibberd, Matthew N. Nelson, Stephen A. Smith
Software Mentions: 1
Published: over 9 years ago

10.1007/s12250-019-00173-6

Pan-Genomic Analysis of African Swine Fever Virus
Cited by: 12
Author(s): Ziming Wang, Lijia Jia, Jing Li, Haizhou Liu, Di Liu
Software Mentions: 1
Published: almost 5 years ago

10.3390/v9030045

Phage Biodiversity in Artisanal Cheese Wheys Reflects the Complexity of the Fermentation Process
Cited by: 18
Author(s): Jennifer Mahony, Angelo Moscarelli, Philip Kelleher, Gabriele Andrea Lugli, Marco Ventura, Luca Settanni, Douwe van Sinderen
Software Mentions: 1
Published: over 7 years ago

10.1016/j.patter.2021.100247

Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19
Cited by: 4
Author(s): Sudhir Ghandikota, Mihika Sharma, Anil G. Jegga
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.1607

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum
Cited by: 60
Author(s): Karthik Anantharaman, Christopher T. Brown, David Burstein, Cindy J. Castelle, Alexander J. Probst, Brian C. Thomas, Kenneth H. Williams, Jillian F. Banfield
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.677

Using network clustering to predict copy number variations associated with health disparities
Cited by: 0
Author(s): Yi Jiang, Hong Qin, Li Yang
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.3243

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect<i>Archaea</i>and<i>Bacteria</i>
Cited by: 199
Author(s): Benjamin Bolduc, Ho Bin Jang, Guilhem Doulcier, Zhi You, Simon Roux, Matthew B. Sullivan
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.415

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
Cited by: 103
Author(s): Christopher W. Beitel, Lutz Froenicke, Jenna M. Lang, Ian F Korf, Richard W. Michelmore, Jonathan A. Eisen, Aaron E. Darling
Software Mentions: 1
Published: over 10 years ago

10.1098/rsta.2019.0394

The parallelism motifs of genomic data analysis
Cited by: 10
Author(s): Katherine Yelick, Aydın Buluç, Muaaz Gul Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven Hofmeyr, Oğuz Selvitopi, Cristina Teodoropol, Leonid Oliker
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12859-016-1078-6

Context-specific functional module based drug efficacy prediction
Cited by: 3
Author(s): Woochang Hwang, Ji Il Choi, Mijin Kwon, Doheon Lee
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-021-04042-6

PIGNON: a protein–protein interaction-guided functional enrichment analysis for quantitative proteomics
Cited by: 4
Author(s): Rachel Nadeau, Anastasiia Byvsheva, Mathieu Lavallée‐Adam
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-8-236

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
Cited by: 245
Author(s): Traver Hart, Insuk Lee, Edward M. Marcotte
Software Mentions: 1
Published: over 17 years ago

10.1186/s12859-017-1668-y

In silico approach to designing rational metagenomic libraries for functional studies
Cited by: 6
Author(s): Anna Kusnezowa, Lars I. Leichert
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-12-339

A comparison of the functional modules identified from time course and static PPI network data
Cited by: 98
Author(s): Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen, Yi Pan
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-12-436

clusterMaker: a multi-algorithm clustering plugin for Cytoscape
Cited by: 482
Author(s): John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2105-10-S12-S6

Clinical bioinformatics for complex disorders: a schizophrenia case study
Cited by: 12
Author(s): Emanuel Schwarz, F. Markus Leweke, Sabine Bahn, Píetro Lió
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2105-15-233

BorreliaBase: a phylogeny-centered browser of Borrelia genomes
Cited by: 32
Author(s): Lia Di, Pedro Pagan, Daniel Packer, Che L. Martin, Saymon Akther, Girish Ramrattan, Emmanuel F. Mongodin, Claire M. Fraser, Steven E. Schutzer, Benjamin J. Luft, Sherwood Casjens, Wei Qiu
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-017-1920-5

RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks
Cited by: 1
Author(s): Osamu Maruyama, Yuki Kuwahara
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12859-018-2362-4

Efficient inference of homologs in large eukaryotic pan-proteomes
Cited by: 9
Author(s): Siavash Sheikhizadeh Anari, Dick de Ridder, M. Eric Schranz, Sandra Smit
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-11-521

Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity
Cited by: 13
Author(s): Jong-Kwang Kim, Kai Tan
Software Mentions: 1
Published: about 14 years ago

10.1186/s12859-018-2123-4

A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration
Cited by: 14
Author(s): Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman K. Halgamuge
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-7-488

Evaluation of clustering algorithms for protein-protein interaction networks
Cited by: 772
Author(s): Sylvain Brohée, Jacques van Helden
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2105-15-335

Detecting temporal protein complexes from dynamic protein-protein interaction networks
Cited by: 66
Author(s): Le Ou-Yang, Dao‐Qing Dai, Xiaoli Li, Min Wu, Xiaofei Zhang, Peng Yang
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2105-10-283

RRW: repeated random walks on genome-scale protein networks for local cluster discovery
Cited by: 161
Author(s): Kathy Macropol, Tolga Can, Ambuj K. Singh
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2105-8-482

Identifying protein complexes directly from high-throughput TAP data with Markov random fields
Cited by: 14
Author(s): Wasinee Rungsarityotin, Roland Krause, Arno Schödl, Alexander Schliep
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2105-11-397

Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes
Cited by: 11
Author(s): Shaoqiang Zhang, Shan Li, Phuc Pham, Zhengchang Su
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-021-04013-x

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation
Cited by: 1
Author(s): Elena Tea Russo, Alessandro Laio, Marco Punta
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-10-169

A core-attachment based method to detect protein complexes in PPI networks
Cited by: 319
Author(s): Min Wu, Xiaoli Li, Chee Keong Kwoh, See-Kiong Ng
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-019-3007-y

Identifying protein complexes based on an edge weight algorithm and core-attachment structure
Cited by: 19
Author(s): Rongquan Wang, Caixia Wang
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2105-13-S10-S18

A methodology for detecting the orthology signal in a PPI network at a functional complex level
Cited by: 12
Author(s): Pavol Jancura, Eleftheria Mavridou, Enrique Carrillo de Santa Pau, Elena Marchiori
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-15-S12-S7

An efficient protein complex mining algorithm based on Multistage Kernel Extension
Cited by: 3
Author(s): Xin Shen, Yanli Zhao, Yanan Li, Tingting He, Jincai Yang, Xiaohua Hu
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2105-16-S12-S5

Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks
Cited by: 4
Author(s): Xin Shen, Lanxing Yi, Yudi Yang, Jincai Yang, Tingting He, Xiaohua Hu
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-12-24

GraphCrunch 2: Software tool for network modeling, alignment and clustering
Cited by: 69
Author(s): Oleksii Kuchaiev, Aleksandar Stevanović, Wayne B. Hayes, Nataša Pržulj
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2105-14-S2-S23

A novel subgradient-based optimization algorithm for blockmodel functional module identification
Cited by: 4
Author(s): Yijie Wang, Xiaoning Qian
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12859-020-03792-z

Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines
Cited by: 0
Author(s): Marcos Viana, Adhemar Zerlotini, Maurício de Alvarenga Mudadu
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2105-15-186

Detecting overlapping protein complexes based on a generative model with functional and topological properties
Cited by: 38
Author(s): Xiaofei Zhang, Dao‐Qing Dai, Le Ou-Yang, Hong Yan
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-13-S3-S10

FUSE: a profit maximization approach for functional summarization of biological networks
Cited by: 25
Author(s): Boon-Siew Seah, Sourav S. Bhowmick, C. Forbes Dewey, Hanry Yu
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-10-99

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
Cited by: 193
Author(s): James Vlasblom, Shoshana J. Wodak
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-017-1726-5

OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement
Cited by: 5
Author(s): Kai Battenberg, Ernest K. Lee, Joanna C. Chiu, Alison M. Berry, Daniel Potter
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-13-109

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data
Cited by: 118
Author(s): Min Li, Xuehong Wu, Jianxin Wang, Yi Pan
Software Mentions: 1
Published: over 12 years ago

10.1186/s12862-019-1394-3

New insights on unspecific peroxygenases: superfamily reclassification and evolution
Cited by: 33
Author(s): Muniba Faiza, Shengfeng Huang, Dongming Lan, Yonghua Wang
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2148-13-261

Contrasting evolutionary patterns of spore coat proteins in two Bacillus species groups are linked to a difference in cellular structure
Cited by: 10
Author(s): Hong Qin, Adam Driks
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12862-016-0684-2

GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm
Cited by: 13
Author(s): Raja Hashim Ali, Sayyed Auwn Muhammad, Lars Arvestad
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2148-12-138

Exploring metazoan evolution through dynamic and holistic changes in protein families and domains
Cited by: 8
Author(s): Zhengyuan Wang, Dante S. Zarlenga, John Martin, Sahar Abubucker, Makedonka Mitreva
Software Mentions: 1
Published: over 12 years ago

10.1186/1742-6405-8-35

Establishment of reference CD4+ T cell values for adult Indian population
Cited by: 36
Author(s): Madhuri Thakar, Philip Abraham, Sunil Arora, Pachamuthu Balakrishnan, Bhaswati Bandyopadhyay, Ameeta Joshi, Kangjam Rekha Devi, Ravi Vasanthapuram, Madhu Vajpayee, Anita Desai, Janardhanan Mohanakrishnan, Kanwar Narain, Koushik Ray, Shilpa S Patil, Ravinder Singh, Anuj Singla, Ramesh Paranjape
Software Mentions: 1
Published: almost 14 years ago

10.1155/2011/743782

ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities
Cited by: 13
Author(s): Dhwani Desai, Soumyadeep Nandi, Prashant K. Srivastava, Andrew M. Lynn
Software Mentions: 1
Published: over 13 years ago

10.1186/1748-7188-7-27

Separating metagenomic short reads into genomes via clustering
Cited by: 18
Author(s): Olga Tanaseichuk, James Borneman, Tao Jiang
Software Mentions: 1
Published: about 12 years ago

10.1186/s12871-017-0421-4

Incidence and severity of postoperative sore throat: a randomized comparison of Glidescope with Macintosh laryngoscope
Cited by: 19
Author(s): Mansoor Aqil, Mueen Ullah Khan, Saara Mansoor, Saad Mansoor, Rashid Saeed Khokhar, Abdul Sattar Narejo
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2105-11-120

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale
Cited by: 56
Author(s): Tamás Nepusz, Rajkumar Sasidharan, Alberto Paccanaro
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-13-S17-S20

B-cell epitope prediction through a graph model
Cited by: 25
Author(s): Liang Zhao, Limsoon Wong, Lanyuan Lu, Steven C. H. Hoi, Jinyan Li
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12859-015-0755-1

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms
Cited by: 14
Author(s): Mohieddin Jafari, Mehdi Mirzaie, Mehdi Sadeghi
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-13-233

Automatic classification of protein structures relying on similarities between alignments
Cited by: 4
Author(s): Guillaume Santini, Henry Soldano, Joël Pothier
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-15-325

MAE-FMD: Multi-agent evolutionary method for functional module detection in protein-protein interaction networks
Cited by: 6
Author(s): Jun Zhong Ji, Lang Jiao, Cui Cui Yang, Jia Lv, Ai Dong Zhang
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2105-11-S1-S11

Fast motif recognition via application of statistical thresholds
Cited by: 8
Author(s): Christina Boucher, James King
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2105-13-S7-S4

An overlapping module identification method in protein-protein interaction networks
Cited by: 5
Author(s): Xuesong Wang, Lijing Li, Yuhu Cheng
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-11-350

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions
Cited by: 49
Author(s): Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto‐Sato, Masaru Tomita
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-14-581

The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide
Cited by: 40
Author(s): Ronan Kapétanovic, Lynsey Fairbairn, Alison Downing, Dario Beraldi, David P. Sester, Tom C. Freeman, Christopher K. Tuggle, Alan Archibald, David Hume
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-15-504

Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes
Cited by: 29
Author(s): Fengming Han, Yong Peng, Lijia Xu, Pei‐Gen Xiao
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-021-07620-3

Protein functional module identification method combining topological features and gene expression data
Cited by: 1
Author(s): Zihao Zhao, Wenjun Xu, Aiwen Chen, Yueyue Han, Shengrong Xia, Chulei Xiang, Chao Wang, Jun Jiao, Hui Wang, Xiaohui Yuan, Lichuan Gu
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-019-5916-6

Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi
Cited by: 12
Author(s): Nicholas Costa Barroso Lima, Arif Mohammad Tanmoy, Emilie Westeel, Luiz Gonzaga Paula de Almeida, Alain Rajoharison, Maksuda Islam, Hubert P. Endtz, Samir K. Saha, Ana Tereza Ribeiro de Vasconcelos, Florence Komurian-Pradel
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-6430-6

The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis
Cited by: 10
Author(s): Arun Kumar Jaiswal, Sandeep Tiwari, Syed Babar Jamal, Letícia de Castro Oliveira, Leandro Gomes Alves, Vasco Azevedo, Preetam Ghosh, Carlo José Oliveira, Siomar C. Soares
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2164-7-298

Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus
Cited by: 21
Author(s): Michael A. Lee, Orla M. Keane, B. C. Glass, T. R. Manley, N. G. Cullen, K. G. Dodds, Alan McCulloch, C. A. Morris, Mark Schreiber, Jonathan Warren, Amonida Zadissa, Theresa Wilson, John C. McEwan
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-13-577

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
Cited by: 180
Author(s): Rolf Sommer Kaas, Carsten Friis, David W. Ussery, Frank Møller Aarestrup
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-10-114

Molecular determinants archetypical to the phylum Nematoda
Cited by: 12
Author(s): Yong Yin, John Martin, Sahar Abubucker, Zhengyuan Wang, Lucjan Wyrwicz, Leszek Rychlewski, James P. McCarter, Richard K. Wilson, Makedonka Mitreva
Software Mentions: 1
Published: over 15 years ago

10.1186/s12864-014-1190-9

Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products
Cited by: 96
Author(s): Xiuna Wang, Xiaoling Zhang, Ling Liu, Meichun Xiang, Wenzhao Wang, Xiang Sun, Yongsheng Che, Liang‐Dong Guo, Gang Liu, Liyun Guo, Chengshu Wang, Wen‐Bing Yin, Marc Stadler, Xinyu Zhang, Xingzhong Liu
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-15-8

ITEP: An integrated toolkit for exploration of microbial pan-genomes
Cited by: 98
Author(s): Matthew N. Benedict, James R. Henriksen, William W. Metcalf, Rachel J. Whitaker, Nathan D. Price
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-10-601

Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor
Cited by: 26
Author(s): Wieslawa I. Mentzen, Matteo Floris, Alberto de la Fuente
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-12-621

Eukaryote DIRS1-like retrotransposons: an overview
Cited by: 38
Author(s): Mathieu Piednoël, Isabelle R. Gonçalves, Dominique Higuet, Éric Bonnivard
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-14-110

Learning contextual gene set interaction networks of cancer with condition specificity
Cited by: 2
Author(s): Sungwon Jung, Michael Verdicchio, Jeff Kiefer, Daniel D. Von Hoff, Michael E. Berens, Michael Bittner, Kim S
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-11-79

Comparative evolutionary analysis of protein complexes in E. coli and yeast
Cited by: 16
Author(s): Adam J. Reid, Juan A. G. Ranea, Christine A. Orengo
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12864-015-1558-5

Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts
Cited by: 43
Author(s): Young-Su Seo, Jae Yun Lim, Jung–Wook Park, Sun‐Young Kim, Hyun‐Hee Lee, Hyeon-Kyoung Cheong, Sang-Mok Kim, Jae Sun Moon, Ingyu Hwang
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-015-1314-x

High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains
Cited by: 33
Author(s): Lin Liu, Wentao Zhu, Zhan Cao, Bin Xu, Gejiao Wang, Meizhong Luo
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-11-S3-S10

Recent advances in clustering methods for protein interaction networks
Cited by: 98
Author(s): Jianxin Wang, Min Li, Youping Deng, Yi Pan
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-15-S6-S8

Gene families as soft cliques with backbones: Amborellacontrasted with other flowering plants
Cited by: 1
Author(s): Chunfang Zheng, A. I. Kononenko, Jim Leebens‐Mack, Eric Lyons, David Sankoff
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-018-4796-5

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
Cited by: 15
Author(s): Ghofran Othoum, Salim Bougouffa, Rozaimi Mohamad Razali, Ameerah Bokhari, Soha A. Alamoudi, André Antunes, Xin Gao, Robert Hoehndorf, Stefan T. Arold, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic̀, Vladimir B. Bajic, Feras F. Lafi, Magbubah Essack
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-6099-x

Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle
Cited by: 6
Author(s): Siqi Tao, Bin Cao, Emmanuelle Morin, Ying‐Mei Liang, Sébastien Duplessis
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-7-100

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria
Cited by: 21
Author(s): Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yuanyuan Li, Jing Hou, Yixue Li, Lei Liu
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-15-S1-S5

Cluster based prediction of PDZ-peptide interactions
Cited by: 17
Author(s): Kousik Kundu, Rolf Backofen
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-017-4243-z

Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales
Cited by: 15
Author(s): Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V. Grigoriev, Antonio G. Pisabarro, Lucı́a Ramı́rez
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-016-2501-0

Hologenome analysis of two marine sponges with different microbiomes
Cited by: 51
Author(s): Tae Woo Ryu, Loqmane Seridi, Lucas Moitinho‐Silva, Matthew Oates, Yi Jin Liew, Charalampos Harris Mavromatis, Xiaolei Wang, Annika F.M. Haywood, Feras F. Lafi, Marija Kuprešanin, Rachid Sougrat, Majed Alzahrani, Emily Giles, Yanal Ghosheh, Celia Schunter, Sebastian Baumgarten, Michael L. Berumen, Xin Gao, Manuel Aranda, Sylvain Forêt, Julian Gough, Christian R. Voolstra, Ute Hentschel, Timothy Ravasi
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-2229-2

Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum
Cited by: 46
Author(s): Priyanka Prasad, Deepti Varshney, Alok Adholeya
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-3927-8

Hybrid assembly with long and short reads improves discovery of gene family expansions
Cited by: 51
Author(s): Jason R. Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P. Walenz, Junqi Liu, Robert M. Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza Maron, Susan R. McCouch, W. Richard McCombie, Michael C. Schatz, Peter Tiffin, Nevin D. Young, Kevin A.T. Silverstein
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-8-320

The extracellular Leucine-Rich Repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns
Cited by: 148
Author(s): Jackie Dolan, Karen Walshe, Samantha Alsbury, Karsten Hokamp, Sean O’Keeffe, Tatsuya Okafuji, Suzanne F.C. Miller, Guy Tear, Kevin J. Mitchell
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-14-186

Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation
Cited by: 125
Author(s): Guoqing Pan, Jianlong Xu, Li Tian, Qingyou Xia, Shao‐Lun Liu, Guojie Zhang, Songgang Li, Chunfeng Li, Handeng Liu, Yang Liu, Shipeng Li, Xi Zhang, Zhengli Wu, Wei Fan, Xiaoqun Dang, Heng Xiang, Meilin Tao, Yanhong Li, Junhua Hu, Zhi Li, Lipeng Lin, Jie Luo, Lina Geng, LinLing Wang, Mengxian Long, Yao Wan, Ningjia He, Ze Zhang, Cheng Lü, Patrick J. Keeling, Jun Wang, Xiang Zhang, Zeyang Zhou
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-S6-S16

A meta-approach for improving the prediction and the functional annotation of ortholog groups
Cited by: 20
Author(s): Cécile Pereira, Alain Denise, Olivier Lespinet
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-9-548

A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao
Cited by: 122
Author(s): Jorge Maurı́cio Costa Mondego, Marcelo Falsarella Carazzolle, Gustavo G.L. Costa, Eduardo Fernandes Formighieri, Lucas Pedersen Parizzi, Johana Rincones, Carolina Cotomacci, Dirce Maria Carraro, Anderson Ferreira da Cunha, Helaine Carrer, Ramón Vidal, Raíssa Estrela, Odalys Águila García, Daniela P. T. Thomazella, Benedito Oliveira, Acássia Benjamim Leal Pires, Maria Carolina Scatolin do Rio, Marcos Renato R. Araújo, Marcos H. de Moraes, Luis A.B. Castro, Karina Peres Gramacho, Marilda Souza Gonçalves, José Pereira Moura Neto, Aristóteles Góes-Neto, Luciana Veiga Barbosa, Mark J. Guiltinan, Bryan A. Bailey, Lyndel W. Meinhardt, Júlio Cézar M. Cascardo, Gonçalo Amarante Guimarães Pereira
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-9-20

Systematic identification of stem-loop containing sequence families in bacterial genomes
Cited by: 5
Author(s): Luca Cozzuto, Mauro Petrillo, Giustina De Silvestro, Pier Paolo Di Nocera, Giovanni Paolella
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12864-019-6234-8

Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes
Cited by: 0
Author(s): Xiao Deng, Xuechao Zhao, Yuan Liang, Liang Zhang, Jianping Jiang, Guoping Zhao, Yan Zhou
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-019-6092-4

Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica
Cited by: 14
Author(s): Yan Qi, Fan Wu, Tiantian Ma, Xifang Zong, Qian Ma, Jie Li, Yufeng Zhao, Yanrong Wang, Jiyu Zhang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-020-07196-4

In silico identification of effector proteins from generalist herbivore Spodoptera litura
Cited by: 6
Author(s): Vinod Kumar Prajapati, Mahendra Varma, Jyothilakshmi Vadassery
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-11-500

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
Cited by: 70
Author(s): Xiangyu Deng, Adam M. Phillippy, Zengxin Li, Steven L. Salzberg, Wei Zhang
Software Mentions: 1
Published: about 14 years ago

10.1186/s12864-018-4836-1

Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases
Cited by: 3
Author(s): Yves Quentin, Patricia Siguier, M. Chandler, Gwennaële Fichant
Software Mentions: 1
Published: over 6 years ago

10.1186/s12920-018-0458-3

Network-based identification of critical regulators as putative drivers of human cleft lip
Cited by: 14
Author(s): Aimin Li, Guimin Qin, Akiko Suzuki, Mona Gajera, Junichi Iwata, Peilin Jia, Zhongming Zhao
Software Mentions: 1
Published: almost 6 years ago

10.1186/1472-6947-13-S1-S5

Improved method for protein complex detection using bottleneck proteins
Cited by: 3
Author(s): Jaegyoon Ahn, Dae Hyun Lee, Yoon Yong-Jin, Yunku Yeu, Sang‐Hyun Park
Software Mentions: 1
Published: over 11 years ago

10.1186/s12866-020-01904-6

Identification of protein complexes and functional modules in E. coli PPI networks
Cited by: 6
Author(s): Ping Kong, Gang Huang, Wei Liu
Software Mentions: 1
Published: over 4 years ago

10.1186/s13104-017-2598-5

Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: “Candidatus Ruthia magnifica”, “Candidatus Vesicomyosocius okutanii” and Thiomicrospira crunogena
Cited by: 4
Author(s): Susan E. McGill, Daniel Barker
Software Mentions: 1
Published: over 7 years ago

10.1186/s13104-015-1476-2

Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer
Cited by: 4
Author(s): J. Robson, Daniel Barker
Software Mentions: 1
Published: about 9 years ago

10.1186/s13104-015-1535-8

A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1
Cited by: 2
Author(s): Kristin M. Wreggelsworth, Daniel Barker
Software Mentions: 1
Published: about 9 years ago

10.1186/1756-0500-5-68

A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags
Cited by: 40
Author(s): Trevor Tyson, Georgina O’Mahony Zamora, Simon Wong, Máirin Skelton, Brian Daly, John T. Jones, Eoin Mulvihill, Benjamin Elsworth, Mark Phillips, Mark Blaxter, Ann M. Burnell
Software Mentions: 1
Published: almost 13 years ago

Projects: cran: MCL

Papers Mentioning MCL 563